← Back to search
9xau

Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA

Method: X-RAY DIFFRACTION Dmax: 125.5 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Citrate synthase 3, peroxisomal

Arabidopsis thaliana

UniProt Q9SJH7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 36–509 Chain B； UniProt 36–509 Not recorded OAA OXALOACETATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；100mM OAA, 65mM HEPES pH 7.0, 6.5mM MgCl2, 13% (w/v) PEG3350 Resolution 1.95 Å R-free 0.225
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 36–509 Chain D； UniProt 36–509 Not recorded OAA OXALOACETATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；100mM OAA, 65mM HEPES pH 7.0, 6.5mM MgCl2, 13% (w/v) PEG3350 Resolution 1.95 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9XAU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9X0I Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and CoA Deposited 2025-09-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–509（474 aa）
Chain B 36–509（474 aa）
Not recorded OAA OXALOACETATE ION × 2 COA COENZYME A × 2 PEG DI(HYDROXYETHYL)ETHER × 2 MG MAGNESIUM ION × 5 EDO 1,2-ETHANEDIOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20mM CoA and 20mM OAA in 90mM HEPES pH7.0, 9mM MgCl2, 18%(w/v) PEG3350
Resolution 1.70 Å R-free 0.197
9XDG Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and MNB Deposited 2025-10-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–509（474 aa）
Chain B 36–509（474 aa）
Not recorded MG MAGNESIUM ION × 2 MNB 5-MERCAPTO-2-NITRO-BENZOIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 OAA OXALOACETATE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM OAA and 10% volume of a saturated solution of DNTB in 70mM HEPES pH7.0, 7mM MgCl2, 14%(w/v) PEG3350
Resolution 2.29 Å R-free 0.266

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CISY3_ARATH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–479； UniProt 36–509 Author chain B； PDBConstruct 6–479； UniProt 36–509 Author chain C； PDBConstruct 6–479； UniProt 36–509 Author chain D； PDBConstruct 6–479； UniProt 36–509

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9xau

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xau
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9xau
Deposition date deposition_date2025-10-23
Structure title titleGlyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA
Keywords keywordscitrate synthase, glyoxysome, glyoxylate cycle, Arabidopsis, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.73 Å
Radius of gyration Rg (electron density) rg_electron38.25 Å
Forward intensity I(0) i0536851000.00
Molecular weight molecular_weight194050.0 kDa
Excluded volume excluded_volume244750 ų
Envelope volume envelope_volume306730 ų
Hydration-shell volume shell_volume64610 ų
Envelope diameter envelope_diameter128.8 Å
Shell Rg shell_rg45.61 Å
Envelope Rg envelope_rg38.27 Å
Shape Rg shape_rg38.24 Å
Total Rg total_rg38.66 Å
Total atoms total_atoms13685
Residues n_residues1744
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax125.5 Å
Rg (real space) rg_real38.66 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real5.3680e+08
I(0) uncertainty (real space) i0_real_error8.4360e+06
Rg (reciprocal space) rg_reciprocal38.71 Å
I(0) (reciprocal space) i0_reciprocal536900000.0000
Solution quality estimate total_estimate0.8834
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.9 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.405
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha196100000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.783
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▶

8. Citations (1)

▶

9. Files and Curves (10)